Chromosomal distribution and relative expression levels of SRS, GRA, and
protein A and D families. The chromosomal position and distribution of SRS (◊), GRA (⎔) and T. gondii protein A and D families (Δ) that are differentially expressed between merozoites and tachyzoites is displayed. Tandemly repeated genes are shown as clusters. Uncoloured genes were not expressed in either tachyzoite or merozoite >stage (RPKM <10). Black coloured genes were not differentially expressed between tachyzoites and merozoites. The shade of red (induced in tachyzoites relative to merozoites) or green (induced in merozoites relative to tachyzoites) indicated the fold increase in expression relative to the other life cycle stage. The chromosomal position of SRS pseudogenes is not displayed. The majority of GRA genes were upregulated in tachyzoites. Only GRA11 gene expression was specifically induced in merozoites. The majority of SRSs were upregulated in merozoites. 52 SRS genes were upregulated in merozoites whereas only 14 were upregulated in tachyzoites. Genes in each cluster tended to be coordinately regulated according to life cycle stage, with only 4 exceptions: One gene in each of the SRS16, SRS36, T. gondii Family A (Chromosome XII) and T. gondii Family D (Chromosome XI) clusters was upregulated in tachyzoites, relative to merozoites.